tbuckley/cabot-search huggingface dataset:
Ventilatory associated barotrauma in COVID-19 patients: A multicenter observational case control study (COVI-MIX-study)
Authors: Luigi Vetrugno, Nadia Castaldo, Alberto Fantin, Cristian Deana, Andrea Cortegiani, Federico Longhini, Francesco Forfori, Gianmaria Cammarota, Domenico Luca Grieco, Miriam Isola, Paolo Navalesi, Salvatore Maurizio Maggiore, Matteo Bassetti, Alfredo Chetta, Marco Confalonieri, Maria De Martino, Giovanni Ferrari, Daniela Francisi, Roberto Luzzati, Simone Meini, Mariano Scozzafava, Emanuela Sozio, Carlo Tascini, Flavio Bassi, Vincenzo Patruno, Edoardo De Robertis, Chiara Aldieri, Lorenzo Ball, Elisa Baratella, Michele Bartoletti, Annalisa Boscolo, Barbara Burgazzi, Vito Catalanotti, Paola Confalonieri, Silvia Corcione, Francesco Giuseppe De Rosa, Alessandro De Simoni, Valerio Del Bono, Roberta Di Tria, Sara Forlani, Daniele Roberto Giacobbe, Bianca Granozzi, Laura Labate, Sara Lococo, Tommaso Lupia, Carola Matellon, Sara Mehrabi, Sabrina Morosi, Silvia Mongodi, Maddalena Mura, Stefano Nava, Riccardo Pol, Tommaso Pettenuzzo, Nguyen Hoang Quyen, Carolina Rescigno, Elda Righi, Barbara Ruaro, Francesco Salton, Silvia Scabini, Angelo Scarda, Marcella Sibani, Evelina Tacconelli, Gennaro Tartaglione, Beatrice Tazza, Eleonora Vania, Pierluigi Viale, Andrea Vianello, Alessandro Visentin, Umberto Zuccon, Francesco Meroi, Danilo Buonsenso
Journal: Pulmonology (2022)

The risk of barotrauma associated with different types of ventilatory support is unclear in COVID-19 patients. The primary aim of this study was to evaluate the effect of the different respiratory support strategies on barotrauma occurrence; we also sought to determine the frequency of barotrauma and the clinical characteristics of the patients who experienced this complication.
Microbial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice
Authors: María A. Núñez-Sánchez, Florence M. Herisson, Jonathan M. Keane, Natalia García-González, Valerio Rossini, Jorge Pinhiero, Jack Daly, Milán Bustamante-Garrido, Cara M. Hueston, Shriram Patel, Nuria Canela, Pol Herrero, Marcus J. Claesson, Silvia Melgar, Ken Nally, Noel M. Caplice, Cormac G.M. Gahan
Journal: Gut Microbes (2022)

The mechanisms by which early microbial colonizers of the neonate influence gut development are poorly understood. Bacterial bile salt hydrolase (BSH) acts as a putative colonization factor that influences bile acid signatures and microbe-host signaling pathways and we considered whether this activity can influence infant gut development. In silico analysis of the human neonatal gut metagenome confirmed that BSH enzyme sequences are present as early as one day postpartum. Gastrointestinal delivery of cloned BSH to immature gnotobiotic mice accelerated shortening of the colon and regularized gene expression profiles, with monocolonised mice more closely resembling conventionally raised animals. In situ expression of BSH decreased markers of cell proliferation (Ki67, Hes2 and Ascl2) and strongly increased expression of ALPI, a marker of cell differentiation and barrier function. These data suggest an evolutionary paradigm whereby microbial BSH activity potentially influences bacterial colonization and in-turn benefits host gastrointestinal maturation.
Second symptomatic COVID-19 infections in patients with an underlying monoclonal gammopathy
Authors: Saurabh Zanwar, Matthew Ho, Francis K. Buadi, Sikander Ailawadhi, Jeremy Larsen, Leif Bergsagel, Moritz Binder, Asher Chanan-Khan, David Dingli, Angela Dispenzieri, Rafael Fonseca, Morie A. Gertz, Wilson Gonsalves, Ronald S. Go, Suzanne Hayman, Prashant Kapoor, Taxiarchis Kourelis, Martha Q. Lacy, Nelson Leung, Yi Lin, Eli Muchtar, Vivek Roy, Taimur Sher, Rahma Warsame, Amie Fonder, Miriam Hobbs, Yi L. Hwa, Robert A. Kyle, S. Vincent Rajkumar, Shaji Kumar
Journal: Blood Cancer Journal (2022)
The pathologic spectrum of adenovirus nephritis in the kidney allograft
Authors: Geetha Jagannathan, Astrid Weins, Emily Daniel, Russel J. Crew, Sidney J. Swanson, Glen S. Markowitz, Vivette D. D’Agati, Nicole K. Andeen, Helmut G. Rennke, Ibrahim Batal
Journal: Kidney International (2022)
Implementation of the NHS-funded tobacco dependence services in England: a qualitative study to understand the contexts of implementation
Authors: Kerry Brennan-Tovey, Maria Raisa Jessica Aquino, Sarah Flanagan, Eileen Kaner, Angela Wearn, Theophile Bigirumurame, Mackenzie Fong, Adam Todd, Paul Aveyard, Kate Jolly, Sarah Damery, Angela Attwood, Debbie Robson, Jane West, Sally Bridges, Christopher J Armitage, Samantha Russell, Steve Strong, Sheena E Ramsay
Journal: The Lancet (2022)
Impact of the temporary suspension of the Bowel Screening Wales programme on inequalities during the COVID-19 pandemic: a retrospective register-based study
Authors: Diana Bright, Jiao Song, Sharon Hillier, Dyfed W Huws, Giles Greene, Karen Hodgson, Ashley Akbari, Rowena Griffiths, Alisha R Davies, Ardiana Gjini
Journal: The Lancet (2022)
Bayesian reconstruction of household transmissions to infer the serial interval of COVID-19 by variants of concern: analysis from a prospective community cohort study (Virus Watch)
Authors: Cyril Geismar, Vincent Nguyen, Ellen Fragaszy, Madhumita Shrotri, Annalan M D Navaratnam, Sarah Beale, Thomas E Byrne, Wing Lam Erica Fong, Alexei Yavlinsky, Jana Kovar, Isobel Braithwaite, Robert W Aldridge, Andrew C Hayward, Peter White, Thibaut Jombart, Anne Cori
Journal: The Lancet (2022)
Changes in diet and physical activity after a pilot intervention to tackle childhood obesity in a deprived inner-London community: an observational cohort study
Authors: Charanpreet Bijlani, Charlotte Vrinten, Kiara Chang, Eva Hrobonova, Ellie Lewis, Paraskevi Seferidi, Anthony Laverty, Cornelia Junghans, Eszter P Vamos
Journal: The Lancet (2022)
Prenatal alcohol prevention in the UK: mapping the landscape through systematic collaborative review
Authors: Cheryl McQuire, Luisa Zuccolo, Felicia Frennesson, Sandra Butcher, Havi Carel, Penny Cook, Tadeas Dvorak, Ellie Gilham, Lisa Hurt, Rebecca Langford, Andrew Misell, Raja Mukherjee, Alice Porter, Oliver Susoy, David Taylor-Robinson, David Troy, Frank de Vocht
Journal: The Lancet (2022)
Implementing behavioural science informed letter interventions to increase COVID-19 vaccination uptake in uncontactable London residents: a difference-in-difference study in London, UK
Authors: Sarah W Huf, Lena Woldmann, Roberto Fernandez Crespo, Kate Grailey, Bahram Hassanpourfard, Matthew Chisambi, Kirstie Black, Joe Nguyen, Bob Klaber, Ara Darzi
Journal: The Lancet (2022)
Systematic review of economic evaluations for internet- and mobile-based interventions for mental health problems
Authors: Fanny Kählke, Claudia Buntrock, Filip Smit, David Daniel Ebert
Journal: npj Digital Medicine (2022)

Abstract In view of the staggering disease and economic burden of mental disorders, internet and mobile-based interventions (IMIs) targeting mental disorders have often been touted to be cost-effective; however, available evidence is inconclusive and outdated. This review aimed to provide an overview of the cost-effectiveness of IMIs for mental disorders and symptoms. A systematic search was conducted for trial-based economic evaluations published before 10th May 2021. Electronic databases (including MEDLINE, PsycINFO, CENTRAL, PSYNDEX, and NHS Economic Evaluations Database) were searched for randomized controlled trials examining IMIs targeting mental disorders and symptoms and conducting a full health economic evaluation. Methodological quality and risk of bias were assessed. Cost-effectiveness was assumed at or below £30,000 per quality-adjusted life year gained. Of the 4044 studies, 36 economic evaluations were reviewed. Guided IMIs were likely to be cost-effective in depression and anxiety. The quality of most evaluations was good, albeit with some risks of bias. Heterogeneity across studies was high because of factors such as different costing methods, design, comparison groups, and outcomes used. IMIs for anxiety and depression have potential to be cost-effective. However, more research is needed into unguided (preventive) IMIs with active control conditions (e.g., treatment as usual) and longer time horizon across a wider range of disorders. Trial registration: PROSPERO Registration No. CRD42018093808.
Imaging endpoints for clinical trial use: a RECIST perspective
Authors: Saskia Litière, Jan Bogaerts
Journal: Journal for ImmunoTherapy of Cancer (2022)

Twenty years after its initial introduction, Response Evaluation Criteria in Solid Tumors (RECIST) remains today a unique standardized tool allowing uniform objective evaluation of response in solid tumors in clinical trials across different treatment indications. Several attempts have been made to update or replace RECIST, but none have realized the general traction or uptake seen with RECIST. This communication provides an overview of some challenges faced by RECIST in the rapidly changing oncology landscape, including the incorporation of PET with 18 F-fluorodeoxyglucose tracer as a tool for response assessment and the validation of criteria for use in trials involving immunotherapeutics. The latter has mainly been slow due to lack of data sharing. Work is ongoing to try to address this.We also aim to share our view as statistician representatives on the RECIST Working Group on what would be needed to validate new imaging endpoints for clinical trial use, with a specific focus on RECIST. Whether this could lead to an update of RECIST or replace RECIST altogether, depends on the changes being proposed. The ultimate goal remains to have a well defined, repeatable, confirmable and objective standard as provided by RECIST today.
Plasma cells: a feasible therapeutic target in pulmonary fibrosis?
Authors: Amanda T. Goodwin, Paul W. Noble, Amanda L. Tatler
Journal: European Respiratory Journal (2022)

<b>Recent work has shown that there are increased plasma cells in IPF and reducing plasma cell numbers can reduce experimental lung fibrosis. This editorial discusses the current knowledge surrounding the role of plasma cells and B-cells in IPF.</b>https://bit.ly/3BQk53K
A Chromosome-Level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation
Authors: Le Wang, May Lee, Zi Yi Wan, Bin Bai, Baoqing Ye, Yuzer Alfiko, Rahmadsyah Rahmadsyah, Sigit Purwantomo, Zhuojun Song, Antonius Suwanto, Gen Hua Yue
Journal: Genomics Proteomics & Bioinformatics (2022)
A blueprint for synthetic control methodology: a causal inference tool for evaluating natural experiments in population health
Authors: Ben Barr, Xingna Zhang, Mark Green, Iain Buchan
Journal: BMJ (2022)

Interventions in emergencies such as the covid-19 pandemic may need rapid supporting evidence. Randomised trials in these situations are often impractical to design or deliver. One technique for estimating the causal effect of an intervention using observational data is the synthetic control method. This article outlines the method and its assumptions, best practice interpretation, and application.
New insight into the application of fluorescence platforms in tumor diagnosis: From chemical basis to clinical application
Authors: Yanchen Li, Qinhua Chen, Xiaoyan Pan, Wen Lu, Jie Zhang
Journal: Medicinal Research Reviews (2022)

Early and rapid diagnosis of tumors is essential for clinical treatment or management. In contrast to conventional means, bioimaging has the potential to accurately locate and diagnose tumors at an early stage. Fluorescent probe has been developed as an ideal tool to visualize tumor sites and to detect biological molecules which provides a requirement for noninvasive, real-time, precise, and specific visualization of structures and complex biochemical processes in vivo. Rencently, the development of synthetic organic chemistry and new materials have facilitated the development of near-infrared small molecular sensing platforms and nanoimaging platforms. This provides a competitive tool for various fields of bioimaging such as biological structure and function imaging, disease diagnosis, in situ at the in vivo level, and real-time dynamic imaging. This review systematically focused on the recent progress of small molecular near-infrared fluorescent probes and nano-fluorescent probes as new biomedical imaging tools in the past 3-5 years, and it covers the application of tumor biomarker sensing, tumor microenvironment imaging, and tumor vascular imaging, intraoperative guidance and as an integrated platform for diagnosis, aiming to provide guidance for researchers to design and develop future biomedical diagnostic tools.
Mitosis domain generalization in histopathology images — The MIDOG challenge
Authors: Marc Aubreville, Nikolas Stathonikos, Christof A. Bertram, Robert Klopfleisch, Natalie ter Hoeve, Francesco Ciompi, Frauke Wilm, Christian Marzahl, Taryn A. Donovan, Andreas Maier, Jack Breen, Nishant Ravikumar, Youjin Chung, Jinah Park, Ramin Nateghi, Fattaneh Pourakpour, Rutger H.J. Fick, Saima Ben Hadj, Mostafa Jahanifar, Adam Shephard, Jakob Dexl, Thomas Wittenberg, Satoshi Kondo, Maxime W. Lafarge, Viktor H. Koelzer, Jingtang Liang, Yubo Wang, Xi Long, Jingxin Liu, Salar Razavi, April Khademi, Sen Yang, Xiyue Wang, Ramona Erber, Andrea Klang, Karoline Lipnik, Pompei Bolfa, Michael J. Dark, Gabriel Wasinger, Mitko Veta, Katharina Breininger
Journal: Medical Image Analysis (2022)
Glycobiology of rheumatic diseases
Authors: Theresa Kissel, René E. M. Toes, Thomas W. J. Huizinga, Manfred Wuhrer
Journal: Nature Reviews Rheumatology (2022)

Glycosylation has a profound influence on protein activity and cell biology through a variety of mechanisms, such as protein stability, receptor interactions and signal transduction. In many rheumatic diseases, a shift in protein glycosylation occurs, and is associated with inflammatory processes and disease progression. For example, the Fc-glycan composition on (auto)antibodies is associated with disease activity, and the presence of additional glycans in the antigen-binding domains of some autoreactive B cell receptors can affect B cell activation. In addition, changes in synovial fibroblast cell-surface glycosylation can alter the synovial microenvironment and are associated with an altered inflammatory state and disease activity in rheumatoid arthritis. The development of our understanding of the role of glycosylation of plasma proteins (particularly (auto)antibodies), cells and tissues in rheumatic pathological conditions suggests that glycosylation-based interventions could be used in the treatment of these diseases. Glycosylation is a common modification that can affect protein stability and interactions. In this Review, the authors discuss the role of glycosylation in rheumatic diseases, as well as the therapeutic potential of glycosylation-based interventions.
The influence of neighbourhood-level socioeconomic deprivation on developing type 2 diabetes in older men: a longitudinal analysis of the British Regional Heart Study cohort data
Authors: Kathryn J Bush, Anna Olia Papacosta, Lucy Lennon, Judith Rankin, Peter Hynes Whincup, Sasiwarang Goya Wannamethee, Sheena Esther Ramsay
Journal: The Lancet (2022)
Quantifying the contribution of poverty and family adversity to adverse child outcomes in the UK: evidence from the UK Millennium Cohort Study
Authors: Nicholas Kofi Adjei, Daniela K Schlüter, Viviane S Straatmann, Gabriella Melis, Kate M Fleming, Ruth McGovern, Louise M Howard, Eileen Kaner, Ingrid Wolfe, David C Taylor-Robinson
Journal: The Lancet (2022)
The evolving landscape of pulmonary arterial hypertension clinical trials
Authors: Jason Weatherald, Athénaïs Boucly, Anthony Peters, David Montani, Krishna Prasad, Mitchell A Psotka, Faiez Zannad, Mardi Gomberg-Maitland, Vallerie McLaughlin, Gérald Simonneau, Marc Humbert
Journal: The Lancet (2022)
How did living in temporary accommodation during the COVID-19 pandemic affect children younger than 5 years' access to health care and health outcomes? A qualitative study of key professionals in a socially and ethnically diverse and deprived area of London
Authors: Diana Margot Rosenthal, Michelle Heys, Antoinette Schoenthaler, Andrew Hayward, Marcella Ucci, Celine Lewis
Journal: The Lancet (2022)
COVID-19 and the role of Voluntary, Community, and Social Enterprises in northern England in responding to the needs of marginalised communities: a qualitative focus group study
Authors: Stephanie Scott, Victoria J McGowan, Josephine M Wildman, Elaine Bidmead, Jane Hartley, Claire Mathews, Becky James, Claire Sullivan, Clare Bambra, Sarah Sowden
Journal: The Lancet (2022)
A partnership approach to supporting the health and wellbeing of the Charedi (Orthodox Jewish) community in London
Authors: Ana Zuriaga, Liam Flannigan, Joanne Wilson, Sarah Weiss, Gitit Rottenberg, Nicole Klynman, Ellen Corine Schwartz, Julie Billett, Jacqueline Katz, Leonora G Weil
Journal: The Lancet (2022)
Challenges and lessons learned from Scotland and England using linked administrative data to evaluate the Family Nurse Partnership: two administrative data cohort studies
Authors: Francesca Cavallaro, Rebecca Cannings-John, Fiona Lugg-Widger, Sally Kendall, Jan van der Meulen, Eilis Kennedy, Emma Howarth, Mike Robling, Ruth Gilbert, Katie Harron
Journal: The Lancet (2022)
How can remote GP consultations be safer?
Authors: Rebecca Rosen, Trisha Greenhalgh
Journal: BMJ (2022)

The safety of remote general practice consultations has been brought into question following the tragic death of David Nash.The student had four telephone consultations but was denied an in-person appointment for a painful ear infection that led to a fatal brain abscess. 1 One senior coroner has voiced concern that this is not an isolated case.In five inquest reports she wrote during the pandemic, she questions whether deaths could have been prevented by in-person consultations. 2 Near universal remote consulting was introduced in March 2020 to minimise the risk of covid-19 infections.By August 2022, 69% of GP consultations in England took place in person. 3 Politicians continue to imply that digital services are more efficient, 4 despite research showing that on average, digital GP consultations take 8% more time than in person, 5 and carry risks including missing safeguarding concerns and delaying diagnoses. 6 7Given these risks, and the mismatch between demand and capacity in general practice, 8 how should appointment type be decided?
Augmenting trauma-focused psychotherapy for post-traumatic stress disorder with brief aerobic exercise in Australia: a randomised clinical trial
Authors: Richard A Bryant, Katie S Dawson, Suzanna Azevedo, Srishti Yadav, Catherine Cahill, Lucy Kenny, Fiona Maccallum, Jenny Tran, Natasha Rawson, Julia Tockar, Benjamin Garber, Dharani Keyan
Journal: The Lancet Psychiatry (2022)
Pelvic pain in transmasculine adolescents receiving testosterone therapy
Authors: Dehlia Moussaoui, Charlotte V. Elder, Michele A. O’Connell, Ashleigh Mclean, Sonia R. Grover, Ken C. Pang
Journal: International Journal of Transgender Health (2022)

Background: Pelvic pain is a common complaint among individuals assigned female at birth. However, few studies have explored pelvic pain among transmasculine patients on gender-affirming testosterone treatment, and most of these were performed in adult populations. Aims: The aim of our study was to investigate the prevalence, risk factors, nature and treatment of pelvic pain among trans adolescents on testosterone. Methods: A retrospective cohort study was performed on all trans adolescents started on gender-affirming testosterone treatment at our institution between 2007 and 2020. Results: Among 158 trans adolescents who were started on testosterone therapy and followed-up for at least six months, 37 (23.4%) reported pelvic pain, with a median interval between testosterone initiation and reported onset of pain of 1.6 months (range 0.3-6.4). The prevalence of pelvic pain was higher in patients who were receiving menstrual suppression (n = 36, 26.3%) compared to those who were not (n = 1, 4.8%), giving a risk difference of 21.5% (95% CI 9.8% to 33.2%, p = 0.028). The most common descriptive terms were "cramps" (n = 17, 45.9%) and "similar to previous period pain" (n = 8, 21.6%). A range of different pharmacological strategies were employed, including paracetamol, NSAIDs, danazol, norethisterone, medroxyprogesterone, etonogestrel implant, intra-uterine device, goserelin and pelvic floor physiotherapy, with variable outcomes. Conclusion: In conclusion, we report here – in what is to our knowledge the first time – the prevalence rate of pelvic pain in trans adolescents on gender-affirming testosterone treatment, and observe that a quarter of them described pelvic pain. Limitations of our study include its retrospective nature, which is likely to be associated with under-reporting of pelvic pain, and the limited documentation of the nature and likely causes of this pain within the medical records. Prospective longitudinal studies to better understand the nature, etiology and optimal management of testosterone-associated pelvic pain are therefore warranted.
m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis
Authors: Ling Wang, Haiyan Zhuang, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang, Jungnam Cho
Journal: Genome biology (2022)

Abstract Heat-imposed crop failure is often attributed to reduced thermotolerance of floral tissues; however, the underlying mechanism remains unknown. Here, we demonstrate that m 6 A RNA methylation increases in Arabidopsis flowers and negatively regulates gene expression variability. Stochastic gene expression provides flexibility to cope with environmental stresses. We find that reduced transcriptional fluctuation is associated with compromised activation of heat-responsive genes. Moreover, disruption of an RNA demethylase AtALKBH10B leads to lower gene expression variability, suppression of heat-activated genes, and strong reduction of plant fertility. Our work proposes a novel role for RNA methylation in the bet-hedging strategy of heat stress response.